4NMM

Crystal Structure of a G12C Oncogenic Variant of Human KRas Bound to a Novel GDP Competitive Covalent Inhibitor

Summary for 4NMM

• Entry DOI: 10.2210/pdb4nmm/pdb
• Related: 4LDJ 4OBE
• Descriptor: GTPase KRas, MAGNESIUM ION, 5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine, ... (4 entities in total)
• Functional Keywords: small gtpase, gdp bound, oncogenic mutation, covalent inhibitor, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human)
• Cellular location: Cell membrane; Lipid-anchor; Cytoplasmic side: P01116
• Total number of polymer chains: 1
• Total formula weight: 19927.51

Authors

Hunter, J.C.,Gurbani, D.,Lim, S.M.,Westover, K.D. (deposition date: 2013-11-15, release date: 2014-06-04, Last modification date: 2024-11-06)

Primary citation

Hunter, J.C.,Gurbani, D.,Ficarro, S.B.,Carrasco, M.A.,Lim, S.M.,Choi, H.G.,Xie, T.,Marto, J.A.,Chen, Z.,Gray, N.S.,Westover, K.D.
In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C.
Proc.Natl.Acad.Sci.USA, 111:8895-8900, 2014

PubMed Abstract: Directly targeting oncogenic V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (K-Ras) with small-molecule inhibitors has historically been considered prohibitively challenging. Recent reports of compounds that bind directly to the K-Ras G12C mutant suggest avenues to overcome key obstacles that stand in the way of developing such compounds. We aim to target the guanine nucleotide (GN)-binding pocket because the natural contents of this pocket dictate the signaling state of K-Ras. Here, we characterize the irreversible inhibitor SML-8-73-1 (SML), which targets the GN-binding pocket of K-Ras G12C. We report a high-resolution X-ray crystal structure of G12C K-Ras bound to SML, revealing that the compound binds in a manner similar to GDP, forming a covalent linkage with Cys-12. The resulting conformation renders K-Ras in the open, inactive conformation, which is not predicted to associate productively with or activate downstream effectors. Conservation analysis of the Ras family GN-binding pocket reveals variability in the side chains surrounding the active site and adjacent regions, especially in the switch I region. This variability may enable building specificity into new iterations of Ras and other GTPase inhibitors. High-resolution in situ chemical proteomic profiling of SML confirms that SML effectively discriminates between K-Ras G12C and other cellular GTP-binding proteins. A biochemical assay provides additional evidence that SML is able to compete with millimolar concentrations of GTP and GDP for the GN-binding site.

PubMed: 24889603
DOI: 10.1073/pnas.1404639111

Experimental method

X-RAY DIFFRACTION (1.89 Å)